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Protein

Cytolethal distending toxin subunit B

Gene

cdtB

Organism
Escherichia coli
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Part of the tripartite complex that is required for the CDT activity. CdtB exhibits a DNA-nicking endonuclease activity, and very probably causes DNA damage in intoxicated cells. This damage induces G2/M cell cycle arrest, chromatin fragmentation, cell distention and nucleus enlargement.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Protein family/group databases

TCDBi1.C.98.1.1. the cytolethal distending toxin (cdt) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytolethal distending toxin subunit B
Short name:
CDT B
Alternative name(s):
Deoxyribonuclease CdtB (EC:3.1.-.-)
Gene namesi
Name:cdtB
OrganismiEscherichia coli
Taxonomic identifieri562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Subcellular locationi

  • Secreted 1 Publication

  • Note: Localized to the nucleus of the infected cells.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi154 – 1541H → A: When the mutant protein is introduced in HeLa cells, it does not result in cell cycle arrest. Devoid of DNA-nicking/DNase activity. 2 Publications
Mutagenesisi229 – 2291D → A: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication
Mutagenesisi260 – 2601D → R: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication
Mutagenesisi261 – 2611H → A: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence analysisAdd
BLAST
Chaini19 – 269251Cytolethal distending toxin subunit BPRO_0000013373Add
BLAST

Interactioni

Subunit structurei

Heterotrimer of 3 subunits, CdtA, CdtB and CdtC.

Structurei

Secondary structure

1
269
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi20 – 223Combined sources
Beta strandi25 – 328Combined sources
Helixi38 – 425Combined sources
Helixi44 – 496Combined sources
Beta strandi56 – 638Combined sources
Beta strandi85 – 906Combined sources
Beta strandi93 – 975Combined sources
Beta strandi99 – 1057Combined sources
Beta strandi109 – 1113Combined sources
Beta strandi116 – 1227Combined sources
Beta strandi125 – 1306Combined sources
Beta strandi140 – 1456Combined sources
Beta strandi148 – 1547Combined sources
Beta strandi157 – 1604Combined sources
Helixi163 – 17513Combined sources
Helixi180 – 1834Combined sources
Beta strandi186 – 1927Combined sources
Helixi197 – 2015Combined sources
Helixi206 – 2105Combined sources
Beta strandi212 – 2154Combined sources
Beta strandi229 – 2379Combined sources
Beta strandi245 – 2484Combined sources
Turni249 – 2524Combined sources
Beta strandi264 – 2674Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2F1NX-ray1.73A19-269[»]
ProteinModelPortaliQ46669.
SMRiQ46669. Positions 19-268.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46669.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi195 – 21016Nuclear localization signalAdd
BLAST

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR003539. CD_toxinB.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
PIRSFiPIRSF018539. CDT_B. 1 hit.
PRINTSiPR01388. CDTOXINB.
SUPFAMiSSF56219. SSF56219. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q46669-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKYIISLIV FLSFYAQADL TDFRVATWNL QGASATTESK WNINVRQLIS
60 70 80 90 100
GENAVDILAV QEAGSPPSTA VDTGTLIPSP GIPVRELIWN LSTNSRPQQV
110 120 130 140 150
YIYFSAVDAL GGRVNLALVS NRRADEVFVL SPVRQGGRPL LGIRIGNDAF
160 170 180 190 200
FTAHAIAMRN NDAPALVEEV YNFFRDSRDP VHQALNWMIL GDFNREPADL
210 220 230 240 250
EMNLTVPVRR ASEIISPAAA TQTSQRTLDY AVAGNSVAFR PSPLQAGIVY
260
GARRTQISSD HFPVGVSRR
Length:269
Mass (Da):29,529
Last modified:November 1, 1996 - v1
Checksum:i958B09BD6C73EBB5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04208 Unassigned DNA. Translation: AAA18786.1.
PIRiI69095.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04208 Unassigned DNA. Translation: AAA18786.1.
PIRiI69095.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2F1NX-ray1.73A19-269[»]
ProteinModelPortaliQ46669.
SMRiQ46669. Positions 19-268.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

TCDBi1.C.98.1.1. the cytolethal distending toxin (cdt) family.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ46669.

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR003539. CD_toxinB.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
PIRSFiPIRSF018539. CDT_B. 1 hit.
PRINTSiPR01388. CDTOXINB.
SUPFAMiSSF56219. SSF56219. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Cloning, sequencing, and expression of the Escherichia coli cytolethal distending toxin genes."
    Pickett C.L., Cottle D.L., Pesci E.C., Bikah G.
    Infect. Immun. 62:1046-1051(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: O128:H- / 9142-88 / EPEC.
  2. "Escherichia coli CdtB mediates cytolethal distending toxin cell cycle arrest."
    Elwell C.A., Chao K., Patel K., Dreyfus L.A.
    Infect. Immun. 69:3418-3422(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF HIS-154.
  3. "DNase I homologous residues in CdtB are critical for cytolethal distending toxin-mediated cell cycle arrest."
    Elwell C.A., Dreyfus L.A.
    Mol. Microbiol. 37:952-963(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-154; ASP-229; ASP-260 AND HIS-261.
  4. "Nuclear localization of the Escherichia coli cytolethal distending toxin CdtB subunit."
    McSweeney L.A., Dreyfus L.A.
    Cell. Microbiol. 6:447-458(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, IDENTIFICATION OF THE NUCLEAR LOCALIZATION SIGNAL.
  5. "Differences in crystal and solution structures of the cytolethal distending toxin B subunit: Relevance to nuclear translocation and functional activation."
    Hontz J.S., Villar-Lecumberri M.T., Potter B.M., Yoder M.D., Dreyfus L.A., Laity J.H.
    J. Biol. Chem. 281:25365-25372(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 19-269.

Entry informationi

Entry nameiCDTB_ECOLX
AccessioniPrimary (citable) accession number: Q46669
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: November 1, 1996
Last modified: October 14, 2015
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The operon of the strain O128:H- / 9142-88 / EPEC is referred to as cdt type II (CDT-II).

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.